REPRODUCE-ME: Ontology-Based Data Access for Reproducibility of Microscopy Experiments

  • Sheeba Samuel
  • Birgitta König-Ries
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10577)


It has always been the aim of every scientist to make their work reproducible so that the scientific community can verify and trust the experiment results. With more complex in vivo and in vitro studies, achieving reproducibility has become more challenging over the last decades. In this work, we focus on integrative data management for reproducibility aspects related to execution environment conservation taking into account the use case of microscopy experiments. We use Semantic Web technologies to describe the experiment and its execution environment. We have developed an ontology, REPRODUCE-ME (Reproduce Microscopy Experiments) by extending the existing vocabulary PROV-O. Scientists can use this ontology to make semantic queries related to reproducibility of experiments on the microscopic data. To ensure efficient execution of these queries, we rely on ontology-based data access to source data stored in a relational DBMS.


Reproducibility Experiments Ontology OBDA Microscopy 



This research is supported by the “Deutsche Forschungsgemeinschaft” (DFG) in Project Z2 of the CRC/TRR 166 “High-end light microscopy elucidates membrane receptor function - ReceptorLight”. Birgitta König-Ries was on sabbatical at DFG FZT 118 iDiv while working on this paper. We thank Christoph Biskup and Kathrin Groeneveld from University Hospital Jena, Germany, for providing the requirements to develop the proposed approach and validating the system and our colleagues Martin Bücker, Frank Taubert und Daniel Walther for their feedback.


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  1. 1.Heinz-Nixdorf Chair for Distributed Information SystemsFriedrich-Schiller UniversityJenaGermany

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